We don’t eliminate uncontacted groups any more because we’ve contacted everyone we want stuff from, and it didn’t work out well for them. Lower technology groups in the 1800’s submitted or were killed off. In a finite universe, any competition could one day try to take you out, so you take them out.
I don’t believe anyone can fathom another alien race, much less assign them ethical rules about interfering with other species. And apes are slowly being driven out of their habitat as we continue to expand.